Thornton Lab

Kevin Thornton's lab at UC Irvine

Books and course materials
Recent posts
Lab policies and procedures manual

Data from Rogers et al. 2014 Manuscript

  1. The bam files that we generated are available from the NCBI Sequence Read Archive (SRA). The accession numbers for the Illumina data are SRP040290 and SRP029453. The PACbio data fall under SRP029453.
  2. Scripts to download the Illumina data from the UCI server
  3. SI material
  4. Source code for PE clustering. Please note that release 0.1.0 corresponds to the precise pipeline used in Rogers et al. (The branch called published_version is also the same code as v0.1.0.) The master branch will likely be further developed to simplify/streamline the pipeline. If you want to reproduce our precise results, use version 0.1.0 AND the precise bwa, samtools, etc. versions described in the Rogers et al. paper!
  5. Info related to visualizing results on the UCSC browser may be found here (Rebekah Rogers’ website).